E. COLI YGJD(E12A)-yeaz heterodimer in complex with ATP

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 24% strand (DSSP).

Ligands and binding sites

• ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
• FE · Fe (III) ion · metal · 2 copies · chains A, B
• ACT · Acetate ion · additive · 2 copies · chains A, C, B
• PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains C, B, D
• GOL · Glycerol · additive · chains C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Interfaces

4 interfaces between chains.

• B–D · 1418 Ų buried · 15 hydrogen bonds · protein-protein
• A–C · 1407 Ų buried · 12 hydrogen bonds · protein-protein
• B–C · 730 Ų buried · 8 hydrogen bonds · protein-protein
• A–D · 411 Ų buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

• 4WQ4 · E. coli YgjD(E12A)-YeaZ heterodimer in complex with ATP · the same entry in another collection · chain A against A, TM-score 1.00
• P05852 · AlphaFold monomer V2.0 prediction for tRNA N6-adenosine threonylcarbamoyltransferase… · a predicted model of the same protein · chain A against A, TM-score 1.00
• P76256 · AlphaFold monomer V2.0 prediction for tRNA threonylcarbamoyladenosine biosynthesis… · a predicted model of the same protein · chain C against A, TM-score 0.97

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P05852
• Every structure of UniProt P76256
• Elsewhere: RCSB PDB 4WQ4 · PDBe 4WQ4 · UniProt P05852 · UniProt P76256